The traditional vernacular houses in Cyprus as houses of ethnic co-existence had witnessed all the tension and sympathy between Turkish and Greek Cypriots, the two natives of the Island. Leaving aside the fact that little is known about these houses, the ethnic conflict which had generated between the Turkish and Greek Cypriots seem to have hindered studies aiming at identifying differences and/or similarities between houses of two communities objectively. In parallel with this, the terms “Greek house”, “Turkish house” or “Ottoman house” are widely used to categorise these houses according to their ethnic occupation at a specific time irrespective of their spatial characteristics. Similarly the description of these houses as “courtyard houses” is another cliché among the architects and scholars who do not explain what that really is other than being “organised around an internal courtyard” and what it is that makes it a “Greek” or a “Turkish” house.This study specifically seeks answer to “how and to what extent ethnic divisions were reflected in their domestic cultures of these groups?” The research sets out exploring similarities and dissimilarities between houses considered as Greek and Turkish and to clarify what makes a house “Turkish” or “Greek”. For this purpose it attempts to give a morphological account for these houses rather than pointing simply to surface characteristics. In doing so it refers to spatial characteristics specifically the relation of internal spaces to each other and the relation of internal spaces to the outside of the dwelling. The study has been grounded on an analytical theory of architecture, which provides tools to represent domestic space and quantify those properties in relation to social variables for a better understanding of the relation between house form and culture. This theory and sets of tools it encapsulates are named as Space Syntax and is based on the idea that cultural information is embedded in the deep abstract structures underlying the actual spatial organisations of the houses named as configuration. With its methodological devices Space Syntax retrieves these underlying regularities that relate directly to the social and cultural functioning of the house. The concepts of spatial configuration and genotype, as invariant properties of these underlying structures are the key concepts adopted in this study. This paper utilises these theoretical and methodological ideas and tools, provided for the analysis of spatial morphology of the built environments and conducts a comparative analysis of traditional domestic spaces to explore the cultural influences. It sets out grasping the spatial themes and/or genotypes as they are called and investigates the way and the degree configuration differs across ethnic groups and finally interprets these for their social implications to throw light whether ethnicity has had any implications on domestic space. The empirical side of the study is based on a comparison of the spatial genotypes discovered, representing a number of rural houses of Greek and Turkish origin selected from one specific region in Cyprus; the Mesarion. These houses, of degrading cultural heritage, were randomly selected based on the availability of identifiable cases. Due to the absence of substantial architectural records, the spatial layouts have generally been reconstructed retrospectively from their present situations through a field study, so as to reflect conditions of the specific period of physical coexistence. This would cover the period dating back to 1900’s until 1974 when the two communities had been separated physically from each other. In total, 60 house layouts have been obtained with 30 Greek and 30 Turkish identity. The plans have then been abstracted according to the principles of the simulation tools, which form the basis for the analysis conducted by using the computer programs developed for this purpose. These abstractions are based on the permeability relations within the house and between the house and its outside world. The paper describes the findings of this empirical study along with the brief explanations of the techniques used and interprets them so as to answer questions of ethnic variations. The analysis has shown that, the terms Greek and Turkish houses are created artificially with political and nationalistic concerns. The houses, as good examples of vernacular, rather than designed, provide us with the necessary information that shows/emphasises the role of peoples’ lifestyles in driving the spatial formations of their dwellings. Ethnicity seems not to have any significant implications for these particular houses at their spatial constitutions at domestic space level. It will be argued once more that, these structures need to be defined in terms of their configurational properties to arrive at a full understanding of the nature of the system which enables the essence of spatial meaning to be understood and to form the basis for comparisons and for further understanding of space use. Surely surface appearances are informative as well, but rather as a ground where tastes and fashion are displayed not as a mirror to cultural structures.